Rather than using a wood pin in your pin-style miter gauge jig, use a piece metal key stock to give yourself a permanent piece to register your cuts.
Box joints make for strong construction, but I always found the pin-style miter gauge jig for my router table fussy to set up. I usually ended up cutting more test pieces than workpieces in order to get the spacing dialed in. Finally, I had a breakthrough: instead of using a wooden pin for the jig, I switched to metal key stock that you can find at a hardware store. Its dimensions match my 1/4″ straight bit exactly. I installed a short piece permanently in the jig to register the cuts. A second, longer piece helps me precisely index the space between the bit and the metal pin during initial setup.
